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RNA Interference

RNA Interference

RNA interference is a process in which translation of some of a cell's messenger RNA (mRNA) sequences is prevented, because of the presence of (and consequent destruction of) matching double-stranded RNA sequences. RNA interference is believed to protect the cell against viruses and other threats. "Interference" refers to the interruption of the cell's translation of its own mRNA. RNA interference is also called posttranscriptional gene silencing, since its effect on gene expression occurs after the creation of the mRNA during transcription.

RNA interference has been found in plants, fungi, and a variety of animals, including the roundworm (Caenorhabditis elegans ), fruit fly (Drosophila melanogaster ), zebrafish, and mouse. It is believed to be an ancient form of defense. It may also explain some or most of the gene-silencing effect of "antisense" RNA, as discussed elsewhere in this encyclopedia.

Dicing up dsRNA

Under most circumstances, RNA in a cell is present as a single-stranded molecule only. For instance, mRNA is created in the cell nucleus and transported to the ribosomes in the cytoplasm as a single strand. Double-stranded RNA (dsRNA), in which two complementary strands pair up, is normally present only in circumstances that pose a threat to the cell. This can occur when a dsRNA virus infects the cell, or from infection by some other viruses whose genomes are temporarily copied into dsRNA. It also occurs when certain types of transposable genetic elements (transposons ) copy themselves in preparation for reinserting elsewhere in the cell's genome. Though the RNA copies are single-stranded, most transposons have sequences at their ends that, when transcribed into RNA, can fold back on themselves to form dsRNA.

When a cell detects dsRNA, it uses a nuclease enzyme to cut it into small fragments, twenty-one to twenty-three nucleotides long (the Drosophila enzyme is whimsically but accurately named "dicer"). This inactivates the RNA, so that it cannot be used to carry out the viral replication cycle or be reinserted into the genome (in the case of a transposon), thus protecting the cell from its harmful effects.

Interference

Degradation of the dsRNA is not the end of the process, however. The presence of these fragments also prevents the expression of mRNA containing the same sequences. That is, if the host cell has used its own gene to create a single-stranded mRNA, and that mRNA is present in the cytoplasm along with dsRNA fragments with matching nucleotide sequences, the mRNA will be degraded, and the protein it codes for will not be made. This is the "interference" that gives the phenomenon its name. Indeed, it was this process that led to the discovery of RNA interference: Scientists found that introducing double-stranded RNA reduced, rather than increased, production of the encoded protein.

Note that not all mRNA activity in the cell is suppressed: Only those mRNAs of similar sequence are targeted. This provides a clue to the mechanism of suppression. Experiments have shown that dicer targets mRNA by using the dsRNA fragments themselves as guides. While the details are not yet clear, it is believed that one side of the dsRNA is matched with the complementary mRNA sequence, making a new dsRNA, which is itself then degraded. This mechanism also allows the process to be self-sustaining, as each new round creates new fragments that can target any new mRNA.

The recognition process also lends further credence to the belief that RNA interference is a protective mechanism. By targeting only mRNA sequences previously identified as double-stranded (and therefore dangerous), a cell can avoid creating proteins that may be derived from viruses, albeit at the risk of turning off one or more of its own genes at the same time.

Research Uses of RNA Interference

Because of its ability to turn off individual gene expression, RNA interference provides a remarkably precise tool for studying the effects of individual genes. There are several ways to deliver dsRNA to cells. It can be injected into a single cell or placed in a viral chromosome that infects the cells being studied. Roundworms will absorb dsRNA if they are soaked in a solution containing it, or if they eat bacteria that contain it.

RNA interference has several advantages over the alternative way of "knocking out" a gene, called gene targeting. Unlike gene targeting, administration of dsRNA does not require long and laborious breeding of the target organism carrying the knockout. Even more importantly, the dsRNA knockout is temporary and can be induced at any stage of the life cycle, rather than exerting its effect throughout life, as with gene targeting. This allows short-term studies of gene effects, a feature particularly valuable for studying development, for instance.

New Developments in dsRNA

Recent research has also shown that a class of similar dsRNA fragments, called small temporal RNAs, play important roles in development in the roundworm, fruit fly, and other animals. Although little is so far known about them, these fragments are made by dicer from the cell's own RNA as a normal part of the developmental process and appear to help control gene expression . This is an exception to the statement that the presence of dsRNA signals a threat to the cell; how these are distinguished from threatening dsRNA is not yet known.

see also Antisense Nucleotides; Fruit fly: Drosophila ; Nucleases; RNA; Post-translational Control; RNA Processing; Roundworm: Caenorhabditis elegans ; Transposable Genetic Elements; Virus.

Richard Robinson

Bibliography

Ambros, Victor. "Development: Dicing up RNAs." Science 293 (2001): 811-813.

Gura, Trisha. "A Silence that Speaks Volumes." Nature 404 (2000): 804-808.

Lin, Rueyling, and Leon Avery. "RNA Interference. Policing Rogue Genes." Nature 402 (1999): 128-129.

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RNA interference

RNA interference (RNAi; post-transcriptional gene silencing) The ability of double-stranded RNA to interfere with, or suppress, the expression of a gene with a corresponding base sequence. The phenomenon occurs in many types of organisms, including plants, fungi, and animals. Double-stranded RNA, which is normally a rarity in cells, is cut into fragments by a ribonuclease enzyme (e.g. Dicer in Drosophila). The fragments, typically 21–25 bp long, are called short interfering RNA (siRNA). The two strands of each fragment partially separate, allowing the antisense strand to bind to a complementary ‘sense’ region of another RNA molecule, such as a messenger RNA (mRNA). This then triggers cleavage of the mRNA at that site, thereby effectively blocking expression of the corresponding gene. It is thought that RNA interference may be a mechanism for the cell to combat infection by certain RNA-containing viruses. Alternatively, the cell may use short single-stranded RNAs, called microRNAs (miRNAs), as a means of regulating gene expression, by effectively targeting certain mRNAs for destruction or by repressing their translation. RNA interference is now used as a powerful and versatile experimental tool to suppress particular genes, as a form of knockout.

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post-transcriptional gene silencing

post-transcriptional gene silencing See RNA interference.

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